Microbial Bioactives
Microbial Bioactives | Online ISSN 2209-2161
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Volume 8 Number 1 2025
REVIEWS (Open Access)
Unraveling Fungal Adaptation and Human Gut Multi-Omics: Insights from the Genus Diaporthe
Taufiq Nawaz 1*, Arnold L. Demain 2* , Bianca McVaugh 3
Microbial Bioactives 8 (1) 1-13 https://doi.org/10.25163/microbbioacts.8110650
Submitted: 16 December 2024 Revised: 10 February 2025 Accepted: 17 February 2025 Published: 19 February 2025
Abstract
The genus Diaporthe, including its anamorph Phomopsis, encompasses a diverse group of fungi with significant ecological, agricultural, and biotechnological implications. These fungi exhibit remarkable adaptability, colonizing a wide range of plant hosts and occasionally affecting human health as opportunistic pathogens. This systematic review and meta-analysis integrates evidence from genomic, transcriptomic, and metabolomic studies to comprehensively characterize the molecular mechanisms underlying Diaporthe adaptation, pathogenicity, and secondary metabolite production. A rigorous literature search was conducted across PubMed, Web of Science, and Scopus, following PRISMA guidelines, yielding 148 relevant studies that met inclusion criteria. Data extraction focused on fungal species, omics methodologies, host interactions, biosynthetic gene clusters, transcriptomic profiles, and metabolomic signatures. Meta-analytic synthesis revealed conserved gene clusters associated with toxin production and enzymatic degradation, highlighting pathways critical for host colonization. Transcriptomic analyses revealed dynamic regulation of virulence genes and host-response factors, while metabolomic studies identified polyketides, terpenes, and other bioactive compounds of ecological and pharmacological relevance. Heterogeneity among studies was addressed using random-effects models, and sensitivity analyses confirmed the robustness of pooled estimates. This integrative approach provides a holistic understanding of Diaporthe biology, revealing intricate host–microbe interactions and potential applications in biotechnology and medicine. The findings underscore the importance of multi-omics strategies for elucidating fungal ecology and provide a foundation for future research to mitigate plant disease and explore novel bioactive metabolites.
Keywords: Diaporthe, Phomopsis, multi-omics, genomics, transcriptomics, metabolomics, fungal pathogenicity, secondary metabolites
References
Ahmed, I., Roy, B. C., Khan, S. A., Septer, S., & Umar, S. (2016). Microbiome, metabolome and inflammatory bowel disease. Microorganisms, 4(2), 20. https://doi.org/10.3390/microorganisms4020020
Alves, V., Zamith-Miranda, D., Frases, S., & Nosanchuk, J. D. (2025). Fungal metabolomics: A comprehensive approach to understanding pathogenesis in humans and identifying potential therapeutics. Journal of Fungi, 11(2), 93. https://doi.org/10.3390/jof11020093
Aujoulat, F., Roger, F., Bourdier, A., Lotthé, A., Lamy, B., Marchandin, H., & Jumas-Bilak, E. (2012). From environment to man: Genome evolution and adaptation of human opportunistic bacterial pathogens. Genes, 3(2), 191–232. https://doi.org/10.3390/genes3020191
Becker, Y., Eaton, C. J., Brasell, E., May, K. J., Becker, M., Hassing, B., ... & Scott, B. (2015). The fungal cell-wall integrity MAPK cascade is crucial for hyphal network formation and maintenance of restrictive growth of Epichloë festucae in symbiosis with Lolium perenne. Molecular Plant-Microbe Interactions, 28(1), 69-85. https://doi.org/10.1094/MPMI-06-14-0170-R
Bills, G. F., & Gloer, J. B. (2016). Biologically active secondary metabolites from the fungi. Microbiology Spectrum, 4(6). https://doi.org/10.1128/microbiolspec.funk-0009-2016
Borenstein, M., Hedges, L. V., Higgins, J. P. T., & Rothstein, H. R. (2009). Introduction to meta-analysis. Wiley. https://doi.org/10.1002/9780470743386
Boussau, B., Karlberg, E. O., Frank, A. C., Legault, B. A., & Andersson, S. G. (2004). Computational inference of scenarios for alpha-proteobacterial genome evolution. PNAS, 101(26), 9722-9727. https://doi.org/10.1073/pnas.0400975101
Brazilian National Genome Project Consortium. (2003). The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability. PNAS, 100(20), 11660-11665. https://doi.org/10.1073/pnas.1832124100
Burisch, J., & Munkholm, P. (2013). Inflammatory bowel disease epidemiology. Current Opinion in Gastroenterology, 29(4), 357–362. https://doi.org/10.1097/MOG.0b013e32836229fb
Cheng, S. C., van de Veerdonk, F., Smeekens, S., Joosten, L. A., van der Meer, J. W., Kullberg, B. J., & Netea, M. G. (2010). Candida albicans dampens host defense by downregulating IL-17 production. The Journal of Immunology, 185(4), 2450-2457. https://doi.org/10.4049/jimmunol.1000355
Chepkirui, C., & Stadler, M. (2017). The genus Diaporthe: A rich source of diverse and bioactive metabolites. Mycological Progress, 16, 477-494. https://doi.org/10.1007/s11557-017-1288-y
Chisholm, S. T., Coaker, G., Day, B., & Staskawicz, B. J. (2006). Host-microbe interactions: Shaping the evolution of the plant immune response. Cell, 124(4), 803-814. https://doi.org/10.1016/j.cell.2006.02.008
Cosnes, J., Gower-Rousseau, C., Seksik, P., & Cortot, A. (2011). Epidemiology and natural history of inflammatory bowel diseases. Gastroenterology, 140(6), 1785–1794. https://doi.org/10.1053/j.gastro.2011.01.055
Crotti, E., Rizzi, A., Chouaia, B., Ricci, I., Favia, G., Alma, A., ... & Cherif, A. (2010). Acetic acid bacteria, newly emerging symbionts of insects. Applied and Environmental Microbiology, 76(20), 6963-6970. https://doi.org/10.1128/AEM.01336-10
Dadachova, E., & Casadevall, A. (2008). Ionizing radiation: How fungi cope, adapt, and exploit with the help of melanin. Current Opinion in Microbiology, 11(6), 525-531. https://doi.org/10.1016/j.mib.2008.09.013
Darfeuille-Michaud, A., Boudeau, J., Bulois, P., Neut, C., Glasser, A. L., Barnich, N., ... & Colombel, J. F. (2004). High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology, 127(2), 412-421. https://doi.org/10.1053/j.gastro.2004.04.061
de Sousa, T., Hébraud, M., Dapkevicius, M. L. N. E., Maltez, L., Pereira, J. E., Capita, R., Alonso-Calleja, C., Igrejas, G., & Poeta, P. (2021). Genomic and metabolic characteristics of the pathogenicity in Pseudomonas aeruginosa. International Journal of Molecular Sciences, 22(23), 12892. https://doi.org/10.3390/ijms222312892
DerSimonian, R., & Laird, N. (1986). Meta-analysis in clinical trials. Controlled Clinical Trials, 7(3), 177–188. https://doi.org/10.1016/0197-2456(86)90046-2
Devkota, S., Wang, Y., Musch, M. W., Leone, V., Fehlner-Peach, H., Nadimpalli, A., ... & Chang, E. B. (2012). Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10−/− mice. Nature, 487(7405), 104-108. https://doi.org/10.1038/nature11225
Dighton, J., Tugay, T., & Zhdanova, N. (2008). Fungi and ionizing radiation from radionuclides. FEMS Microbiology Letters, 281(2), 109-120. https://doi.org/10.1111/j.1574-6968.2008.01076.x
Egger, M., Davey Smith, G., Schneider, M., & Minder, C. (1997). Bias in meta-analysis detected by a simple, graphical test. BMJ, 315(7109), 629–634. https://doi.org/10.1136/bmj.315.7109.629
Ellinghaus, D., Bethune, J., Petersen, B. S., & Franke, A. (2015). The genetics of Crohn’s disease and ulcerative colitis—Status quo and beyond. Scandinavian Journal of Gastroenterology, 50(1), 13-23. https://doi.org/10.3109/00365521.2014.990507
Fang, X., Qin, K., Li, S., Han, S., & Zhu, T. (2020). Whole genome sequence of Diaporthe capsici, a new pathogen of walnut blight. Genomics, 112(5), 3751-3761. https://doi.org/10.1016/j.ygeno.2020.03.016
Fiocchi, C. (2012). Genes and ”in-vironment”: How will our concepts on the pathophysiology of inflammatory bowel disease develop in the future? Digestive Diseases, 30(1), 2-11. https://doi.org/10.1159/000341117
Gomes, R. R., Glienke, C., Videira, S. I., Lombard, L., Groenewald, J. Z., & Crous, P. W. (2013). Diaporthe: A genus of endophytic, saprobic and plant pathogenic fungi. Persoonia, 31, 1-41. https://doi.org/10.3767/003158513X666844
Goodwin, S., McPherson, J. D., & McCombie, W. R. (2016). Coming of age: Ten years of next-generation sequencing technologies. Nature Reviews Genetics, 17(6), 333-351. https://doi.org/10.1038/nrg.2016.49
Higgins, J. P. T., Thomas, J., Chandler, J., Cumpston, M., Li, T., Page, M. J., & Welch, V. A. (2022). Cochrane handbook for systematic reviews of interventions (Version 6.3). Cochrane. http://www.training.cochrane.org/handbook
Higgins, J. P. T., Thompson, S. G., Deeks, J. J., & Altman, D. G. (2003). Measuring inconsistency in meta-analyses. BMJ, 327(7414), 557–560. https://doi.org/10.1136/bmj.327.7414.557
Hilário, S., & Gonçalves, M. F. M. (2023). Mechanisms underlying the pathogenic and endophytic lifestyles in Diaporthe: An omics-based approach. Horticulturae, 9(4), 423. https://doi.org/10.3390/horticulturae9040423
Hilário, S., Gonçalves, M. F. M., Fidalgo, C., Tacão, M., & Alves, A. (2022). Genome analyses of two blueberry pathogens: Diaporthe amygdali CAA958 and Diaporthe eres CBS 160.32. Journal of Fungi, 8(8), 804. https://doi.org/10.3390/jof8080804
Hosseini, B., Voegele, R. T., & Link, T. I. (2020). Establishment of a quadruplex real-time PCR assay to distinguish the fungal pathogens Diaporthe longicolla, D. caulivora, D. eres, and D. novem on soybean. PLoS ONE, 16(10), e0257225. https://doi.org/10.1371/journal.pone.0257225
Janda, J. M., & Abbott, S. L. (2010). The genus Aeromonas: Taxonomy, pathogenicity, and infection. Clinical Microbiology Reviews, 23(1), 35-73. https://doi.org/10.1128/CMR.00039-09
Jansson, J., Willing, B., Lucio, M., Fekete, A., Dicksved, J., Halfvarson, J., ... & Schmitt-Kopplin, P. (2009). Metabolomics reveals metabolic biomarkers of Crohn’s disease. PLoS ONE, 4(7), e6386. https://doi.org/10.1371/journal.pone.0006386
Kappelman, M. D., Rifas-Shiman, S. L., Kleinman, K., Ollendorf, D., Bousvaros, A., Grand, R. J., & Finkelstein, J. A. (2007). The prevalence and geographic distribution of Crohn's disease and ulcerative colitis in the USA. Clinical Gastroenterology and Hepatology, 5(12), 1424–1429. https://doi.org/10.1016/j.cgh.2007.07.012
Kiel, A., Creutz, I., Rückert, C., Kaltschmidt, B. P., Hütten, A., Niehaus, K., Busche, T., Kaltschmidt, B., & Kaltschmidt, C. (2022). Genome-based analysis of virulence factors and biofilm formation in novel P. aeruginosa strains isolated from household appliances. Microorganisms, 10(12), 2508. https://doi.org/10.3390/microorganisms10122508
Molodecky, N. A., Soon, I. S., Rabi, D. M., Ghali, W. A., Ferris, M., Chernoff, G., Benchimol, E. I., Panaccione, R., Ghosh, S., Barkema, H. W., et al. (2012). Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review. Gastroenterology, 142(1), 46–54. https://doi.org/10.1053/j.gastro.2011.10.001
Ng, S. C., Bernstein, C. N., Vatn, M. H., Lakatos, P. L., Loftus, E. V., Jr., Tysk, C., O'Morain, C., Moum, B., Colombel, J. F., & Crohn's and Colitis Foundation of Canada. (2013). Geographical variability and environmental risk factors in inflammatory bowel disease. Gut, 62(4), 630–649. https://doi.org/10.1136/gutjnl-2012-303661
Page, M. J., McKenzie, J. E., Bossuyt, P. M., Boutron, I., Hoffmann, T. C., Mulrow, C. D., Shamseer, L., Tetzlaff, J. M., Akl, E. A., Brennan, S. E., Chou, R., Glanville, J., Grimshaw, J. M., Hróbjartsson, A., Lalu, M. M., Li, T., Loder, E. W., Mayo-Wilson, E., McDonald, S., … Moher, D. (2021). The PRISMA 2020 statement: An updated guideline for reporting systematic reviews. BMJ, 372, n71. https://doi.org/10.1136/bmj.n71
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